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The human gut is host to about 100 trillion bacterial cells, about 10 times the number of human cells in the entire body. A quart of seawater contains about 1 billion bacteria cells from 400,000 different species.

Yet we know almost nothing about most of the microbes.

How do they interact with each other? Do they make toxins, break down oils, kill pathogens or contribute to climate change? Could they help save an endangered animal?

Now, a global network of scientists, including some in San Diego County, is trying to catalog the genetic maps of the 5 million species of bacteria that occupy every corner of the planet — deserts, oceans, crop fields, mountain rocks, sea floors, prairies, suburban backyards, high-altitude winds and even the feces of animals.

The ambitious effort, known as the Earth Microbiome Project, promises to revolutionize microbiology just as the field was permanently altered by the creation of the microscope, the development of cell culturing techniques and the discovery of pasturization.

The process undertaken by the project even has a name: metagenomics.

“It truly is the new science of the 21st Century,” said John Wooley, a professor of bioinformatics and computational biology at the University of California San Diego.

Those samples are being sequenced on HiSeq 2000 machines made by San Diego-based Illumina and located at participating U.S. research labs and BGI, one of the world’s largest genetic sequencing centers in Shenzhen, China.

Illumina has led the way in reducing the time it takes to sequence organisms and dramatically lowering the cost for the work, essential developments for making the microbiome project possible.

“We can sequence DNA from a billion cells in one sample for about $15,000,” said Jack Gilbert, one of the project’s leaders and an environmental microbiologist at the Department of Energy’s Argonne National Laboratory in suburban Chicago. “That’s a game changer.”

It’s surprising we know so little about microbes.

Early forms of bacteria were crawling across the earth more than 3 billion years ago, and they play a role in nearly every aspect of life on the planet.

Without the bugs, our skin would be vulnerable to fungal and yeast infections, we wouldn’t be able to digest food, and our bodies would be consumed by disease.

Yet, scant funding has gone to microbial research.

Perhaps that’s because microbiology lacks the same appeal of other sciences, such as space exploration, medicine and computer engineering.

For most people, just the mention of the word microbe conjurs thoughts of diseases and filth. They forget or ignore the many benefits that come from bacteria, such as turning milk into cheese and yogurt, creating antibiotics and other drugs, decomposing dead animals, assisting in the digestion of food and trapping nitrogen in the soil that feeds plants.

Gilbert is hoping that the microbiome project will boost the image of single-cell organisms and draw more people to the metagenomic field.

In San Diego, the project is collecting samples and swabs taken from the fur, skin, ears, mouths and noses of a range of animals at the city’s zoo, Gilbert said.

Eric Allen, an assistant professor at the Scripps Institution of Oceanography in La Jolla, has spent the last four years working on his own small piece of the microbiome at Lake Tyrrell, a shallow salt-crusted area in southeastern Australia.

While a typical one-liter sample of seawater contains several hundred species of bacteria, a similar sample taken from Lake Tyrrell contains only 20 varieties of the organism. That’s because most microbes aren’t able to live in such a harsh, high-saline environment.

So far, Allen has pieced together the DNA sequences of 11 bacteria that thrive in the lake’s salt-crystal rocks.

The information one day might reveal specific salt-tolerent genes that could be used to engineer crops able to grow in high-saline soil that normally wouldn’t support agriculture.

Such efforts are inevitable in Southern California where salt levels will rise as fresh water sources dry up, Allen said.

He and his team have discovered two entirely new versions of bacteria at the Lake Tyrrell — nanosalina and nanosalinarum.

“We really don’t know what they do, but they must be doing something because they are up to 25 percent (of the microbe population) in hyper-saline habitats,” he said.

One clue might come from a light-sensing protein molecule found in the bugs.

“It’s probably for UV protection,” Allen said.

Radiation from the sun can damage the DNA in microbes just as it can in human cells. Having cells that turn UV protection on and off based on the detection of light could allow the bacteria to spend more of their energy at night on other functions, the researcher said.

So far, the Earth Microbiome Project has collected 70,000 samples from 72 investigators in 17 countries, Gilbert said. About 156,000 bacteria species have been genetically identified.

The initial work is being funded by the Department of Energy through its Argonne lab and the Lawrence Berkeley National Laboratory in Berkeley. Corporate sponsors, including Illumina and Mo-Bio, are providing in-kind support.

Another San Diego group is helping to make sense of the mountain of DNA data being gathered by the project.

The Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis, or CAMERA, will dump the sequencing information into its supercomputer data bases, which use sophisticated programs to make data searchable by researchers worldwide, said Wooley, its chief scientific officer.

CAMERA is housed at UCSD’s Atkinson Hall within the California Institute for Telecommunications and Information Technology.

“The (microbiome project) data will be coupled with environmental information — where did the sample come from, what were the conditions, was it from the gut of a termite or collected during a particular weather condition,” Wooley said. “People can put this information together with the sequence data to better understand the microbes.”

It’s too early to guess what kinds of breakthroughs might come from the work, he said.

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